The SequentialLayer was introducing more problems than the ones it solved.
Unfortunately, the old checkpoints will not be compatible but they can be easily converted using:
old_model = tf.keras.models.load_model(".../old_checkpoint")
new_model = bob.learn.tensorflow.models.incepetion_resenet_v2.IncepetionResnetV2()
new_model.set_weights(old_model.get_weights)
new_model.save(".../new_checkpoint")